Favored Son
by Drakai
Summary: Atlantis was a city, just like any other. I mean sure, it did have superior technology, and sure, it did contain a lot of information about the Ancients. And, granted, there was that chill down your back you might get walking through its hallways alone at night. But Atlantis wasn't alive. Was it?
1. Chapter 1

Granted, when all was said and done, flying a Puddlejumper armed with a semi-functioning nuke into a Wraith Hiveship _may_ not have been the best idea he ever had. But he believed it was necessary.

When John Sheppard had stumbled into an expedition to the famed Lost City of Atlantis, inadvertently saving a General's life in the process, he honestly hadn't known if he should accept Dr. Weir's invitation. Even the gentle nudging from General O'Neill (the General he'd saved earlier that day; strange guy) wasn't doing much to make up his mind. Aliens, spaceships, intergalactic gates, it all seemed too much. So he decided to fall back on his old coin, the one he would always use when faced with impossible decisions. It had never failed him before. Except that one time when he had just joined the Air Force. And that one time in Afghanistan. And that time in Antarctica, when he almost got court marshaled.

Come to think of it, maybe he should replace the thing.

Anyway, the _trusty_ coin had been inconclusive the first time (slipping out of his hand and falling edge-firls into a crack in the ground) he flipped it again. And again just to be sure. When it landed heads again, he quickly packed what little things he was allowed to take with him and set off to Colorado. In hindsight, perhaps trusting his future to an inanimate object wasn't the smartest thing to do.

When he'd first laid eyes on Colonel Marshall Sumner he just knew the Atlantis Military Leader would be trouble. And, of course, the man disliked him from their first conversation. For a moment he thought about bringing up Ferris Wheels, or maybe college football, but decided against it. Best not to play the fool _just_ yet.

Luckily for him Dr. Weir, the _actual_ head of the Expedition, had taken somewhat of a liking for him. He'd like to think it was his natural charm and good looks, but he was pretty sure it had more to do with making the chair-thing in Antarctica all glowy.

When he stepped into the wormhole-like standing pond, which one of the younger Lieutenant had told him would hurt (it didn't, it was just very cold) and arrived at the city of Atlantis. Which was several hundred feet below the surface and was quickly losing power to the shield which held all the soggy wetness back. And, to make matters worse, the first planet in the other Galaxy they had went to had his Sheppard luck kick in true to form: get captured by a few space . _Gothic_ space vampires. Just fantastic.

After killing space-Dracula's bride and waking up her entire species, managing to (sort of) lose Col. Sumner in the process, he had assumed command of the military contingent of the expedition and went to try to right his wrongs. Granted Dr. Weir, cool as she was, was still a civilian, so he had to teach her a few things about not leaving people behind. But they got over that quickly enough.

But the city itself was amazing. At times he felt like it would read his mind, since the doors and lights would always do what he wanted them before he would even know he did. And the Puddlejumper handled like a thought, _with a thought_. There was definitely something about the place. At times it was almost like a presence at the back of his mind, comforting and guiding him.

The other Galaxy's races (Pegasus, he would remind himself) were strange, and strangely human. Maybe it was something about the frame, but everything there was on two legs and trying to kill them. From the Hoffans (what kind of a name was that, anyway), with their _science_ to the Genii, with actual pipe-like weapons. He had somehow even managed to make a few lifelong personal enemies (Kolya of the Genii came to mind), and even getting a few random flings with space-babes (who could blame them, he was quite irresistible; and Rodney was just jealous, whatever he may say).

Wait… was his life flashing before his eyes? He groaned, hoping he wouldn't see _those_ moments again. He didn't enjoy it enough the first time around.

So that was where he was now. Two massive Wraith Hiveships bearing down on a mostly-defenseless Atlantis. The brand-new military commander sent by Earth, a Col. Everett (Sumner's old friend, who kinda hated him for the whole 'shooting him' thing), accompanied by useful weapons and poorly though out strategies, was somewhere down there, probably fighting many of the Wraith in the city. His friends looking up at him for salvation (he could even swear Elizabeth had a tear in her eye) and him flying an untested and poorly-constructed (according to Rodney) nuclear bomb into one ship. Even if he did destroy the thing someone else would have to fly another Jumper up to the second Hive. Provided, of course, the Wraith do not wise up to their plans.

 _Well, I guess this is it._ He thought grimly, sending one last longing glance at the city, feeling an echo of sadness at the back of his mind. _Goodbye cruel world. At least I'm going out with a bang._

"Major Sheppard, de-cloak your jumper."

Then again, maybe not.

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 **I like Stargate Atlantis, and Sheppard is my favorite character. That being said, I really don't get the whole 'whump' thing. I mean, I know what it is, but I don't get the appeal of torturing your favorite character.**

 **Since this first chapter is kinds short, and just the retelling of the first season, I'll be posting the second one immediately.**

 **In my not so humble opinion there is something special with Johns ATA-gene, so there will be a lot of that in this story.**

 **And as the first SGA and second non-Naruto story overall, I'd like to know what you think.**


	2. Chapter 2

To say John Sheppard was surprised with the sudden demand may have been a _slight_ understatement. Still, he had learned to grow weary of sudden voices appearing.

"Huh? Who the hell's this?"

"Authentication Alfa Charlie One. De-cloak _now_." The voice was losing patience with him. But what the hell, he was about to die anyway. Why not trust the strange voice with USAF codes. With a mental command the Jumper became visible just as it entered the Hive, and with a strong white light he disappeared.

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Back on Atlantis Dr. Elizabeth Weir, Dr. Rodney McKay and Dr. Carson Beckett (each with their own separate fields, no less) were in the control room, silently watching the screen as a nearby technician counted down to the explosion.

"Detonation in five, four, three, two…" He trailed off as the blip on the radar signifying one of the Hives disappeared. "Target has been neutralized."

"He did it." Elizabeth couldn't believe John was gone, sacrificing his life for theirs."

"Yeah." Dr. McKay sighed softly. "He did."

"Doctor Weir, I'm reading picking up another ship."

"Wraith?"

"Negative, ma'am, I'm reading I.F.F."

 _-Atlantis, this is Sheppard,_

"John?" Elizabeth's voice had a strange mixture of relief, fear and anger.

 _-How many Sheppard's do you know?_

"Oh thank God." The Scottish M.D. sighed in relief.

"No, no, no, this can't be. We saw the Hive blow up." If Rodney didn't know any better, he would swear he was saved a biting remark by another voice.

 _-I assure you Dr. McKay that Major Sheppard is alive and well.-_

"And who is this?" Elizabeth raised a delicate eyebrow at the sky.

 _-Colonel Steven Caldwell, commander of the Daedalus. We are ready to assist you.-_

"We are very glad to hear that Colonel." Elizabeth smiled, ignoring Rodney, who had sunk down to the floor in relief. "And I assume we have you to thank for saving out Major?"

 _-We were monitoring your transmissions as soon as we came out of hyperspace. We couldn't beam him until he disabled his cloak.-_

 _-It didn't take that much convincing, honestly.-_ John's voice cut through. _-Where are we, Elizabeth?-_

"There are still Wraith in the city."

 _-As soon as we deal with this other Hiveship we'll come to assist you.-_ Col. Caldwell spoke up. _-Dr. McKay?-_ All eyes turned to the half-asleep scientist as he jerked to his feet, blinking himself awake.

"What? Yes. Here. I mean, present."

 _-I trust you know what to do with this.-_ A moment after two marines appear in a bright light with a large metallic box between them.

"Is that…?"

"Your ZPM, sir." One of them said, gesturing to the box.

"Now how did they do that?" Carson muttered to himself confused.

"The Daedalus is loaded with Asgard technology. The beaming technology is only the first part of it. They have things like…"

 _-Rodney, would you mind shutting up and plugging in the damned thing?-_

"Yeah, yeah, I'm on it." He pulled the large orange crystal from its box with an almost childlike glee, "Shall we?"

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"Sir, we have bandits bearing three-two-zero."

"All forward rail guns stand by. Launch all fighters."

The space battle was going as well as could be expected. The Daedalus had superior shields and weaponry, but the Hiveship had a lot of Darts that they used to intercept the nuclear warheads before they could get to it. John was the first to admit that the Colonel was a stubborn man, but enough was enough.

"Colonel, you're wasting ordinance. The missiles'll never get through."

"Then what do you propose." He had a feeling this military commander didn't like him, either.

"Why don't you just beam a warhead into the other Hive, like you got me out?"

"The Asgardians built fail-safes into their technology. We can't transport something like hat."

"We have one of these Asgard onboard, right? Just get him to override the fail-safes."

"And why would he do something like that?" Caldwell raised an eyebrow. Maybe John was just imagining it, but the Colonel managed to make even that gesture condescending.

"His ass is on the line, same as ours." The Major deadpanned, looking straight at the senior officer. Steven gazed at him for a few moments before pushing a button on his chair.

"Novak, this is Col. Caldwell. Prepare a warhead for beaming."

 _-Uh, sir… Hermiod's not gonna like this.-_

"I am well aware, Doctor. Make it happen."

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"Wait, what's this?" After instructing Dr. Radek Zelenka about the shield activation, Rodney went to finally install their precious source of power, met by _only_ two marines at the stairs. "This is my escort?"

"I don't know if you noticed byt we're stretched a little thin at the moment." Elizabeth had definitely been spending too much time with Sheppard. Not that he'd say that out loud. To either one.

He liked his limbs exactly where they were, thank you very much.

"Fine. But if we run into danger you have to protect me with your lives."

"Rodney!"

"I mean the ZPM, you have to protect the ZPM with your lives. And also me." Elizabeth looked like she wanted to reprimand him again but settled against it. "What? Am I wrong?"

"Just get going Rodney."

"Fine, bully the brilliant scientist who's about to save your lives."

"Rodney!"

"Fine, fine. After you two." The two marines exchanged glances and set off in a random direction.


	3. Chapter 3

Two lefts and three rights later the two marines were completely confused. Which was perfectly natural. The only ones who could get around the crazy city without any help were Dr. McKay and, to a slightly greater extent, Major Sheppard. It also had the added benefit of making said doctor shut up, and lead the way.

"We're close." McKay grunted, taking a left. "Just a little further up a… Oh, no." The three men stopped, staring at a company of at least a half a dozen Wraith, all with their stunners pointed at them. Without missing a beat Rodney jumped behind a nearby crate and the two marines opened fire taking down two of the Wraiths in their first volley.

However, that still left at least a couple more. Rodney forced himself to look up from behind the crate when one of the marines fell, leaving the other alone with at least four other Wraith. The Canadian doctor cursed himself when he remembered that he had a gun. Another two Wraith fell, but the last two managed to hit the marine before Rodney could get the handgun out of its holster.

"Ah!" He gasped, standing up and pointing the gun at the two remaining space vampires. "You want some of this, huh?" He pressed a button and with an audible _click_ the gun's clip fell down to the floor. "Aw crap." The two Wraith started to slowly approach him. "Wait, stop, don't eat me."

The Wraith stopped; exchanging glances, and then fell down one by one in a small flash of pale blue light, leaving Teyla standing victoriously behind them with one of their own stunners in hand.

"Are you well, Dr. McKay?"

"Yeah, I'm fine." The Canadian slowly sank down to his knees.

"Are you not forgetting something?" He raised an eyebrow at her. "The ZPM?"

"Right." Rodney slowly stood up, grabbing the box. "Come on, you'll have to protect me with…"

"Yes, I know that by now."

"Right. That way." He pointed forward.

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 _-Beaming in three… two… one… Warhead deployed, sir.-_

Major Shepard and Colonel Caldwell watched with baited breaths as, for a moment, nothing happened, before the second Hive ship blew up in a spectacular fashion.

"Huh, it worked." Shepard grinned. "And look, the other Hive's turning tail."

"He's right sir, they're opening up a hyperspace window."

"Only, we have another problem now." Shepard muttered. Caldwell turned to where he was looking at and saw the debris from the detonated ship rush towards the city below.

"Yes, I think you're right."

"Atlantis this is Shepard. You have a lot of debris coming your way; you're toast if you don't get the shield up now."

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 _-Rodney, debris incoming, we need that shield.-_

"Yes, I heard you the first time." The scientist grunted as he hefted the orange crystal onto the machine, aiming it at one of the slots.

 _-Any time now.-_

"Alright, everybody shut up before I snap." He turned the crystal.

 _-Rodney!-_

"Alright, snap! Is everybody happy now?" With a small whoosh the crystal sank halfway into its slot. "Huh, it worked."

 _-The shield's till not up, Rodney, and we're running out of time._

"I know! Just give me a few moments." He turned the orange crystal again, this time in the opposite direction, and it sank in. "Alright, hit it."

The orange glow of the shield enveloped the city at a moderate pace, and not a moment too soon, judging by the large chunks of spaceship that impacted it a second later.

 _-Alright, well done Rodney.-_

"Heh." The scientist sank down to the floor again, closing his eyes blissfully. "I am going to curl up in my bed and sleep for a week." Teyla looked at him with a raised eyebrow.

"Shall I tell the other Wraith that are still left in the city that you are unavailable, then?"

"Right, those guys. Help me up."

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Back at the control room everybody let out a breath of relief. Elizabeth herself leaned on a nearby console allowing herself a few seconds of relief before the fighting resumed.

 _-Atlantis, this is Caldwell.-_

"We read you Colonel. We're just fine." She let out a small smile.

 _-That's nice. You might want to prep your med bay.-_

"Why? What's wrong with yours?" Although she had a familiar foreboding feeling.

 _-It's Shepard, Dr. Weir. He fainted.-_

And there it was.

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 **I know its short, shut up.**


End file.
